BN1805 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 1.6448e-06 7.0105e-04
Layer 4 2.0274e-06 6.8703e-05
Layer 2 3.4279e-06 7.8775e-03
Layer 5 2.2172e-04 1.4501e-03
Layer 6 2.6245e-04 1.1257e-03
Layer 1 9.1280e-01 5.6429e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.4180 0.7112
RAB3A Layer 4 2.2969 0.7013
ATP5F1D Layer 4 2.1621 0.6956
SH3GL2 Layer 5 2.3711 0.6955
PINK1 Layer 6 2.5176 0.6953
NDRG4 Layer 5 2.2266 0.6943
MAPK10 Layer 4 2.4395 0.6933
NAPB Layer 5 2.1875 0.6921
CHGA Layer 5 2.6191 0.6920
COX5A Layer 5 2.2168 0.6906
GHITM Layer 6 2.3262 0.6880
PPP3R1 Layer 6 2.2803 0.6878
ATP6V1A Layer 6 2.4121 0.6877
VDAC2 Layer 4 2.5449 0.6877
INA Layer 3 2.2129 0.6874
CEND1 Layer 6 2.3643 0.6874
ATP1A1 Layer 4 2.1094 0.6830
MDH1 Layer 4 2.0352 0.6827
BEX2 Layer 6 2.1250 0.6825
GOT1 Layer 6 2.4570 0.6802
SYNGR1 Layer 4 2.5059 0.6800
MAP1LC3B Layer 4 2.1973 0.6798
PACSIN1 Layer 4 2.2969 0.6798
PDCD5 Layer 4 2.2930 0.6790
SYP Layer 5 2.1543 0.6782
CALY Layer 3 2.1914 0.6779
C12orf57 Layer 6 2.2578 0.6777
CAPNS1 Layer 6 2.3086 0.6771
DNAJC6 Layer 6 2.1699 0.6770
TPPP Layer 5 2.1973 0.6764
G3BP2 Layer 6 2.3213 0.6761
DYNLRB1 Layer 5 2.1123 0.6744
TAGLN3 Layer 5 2.4297 0.6742
GNG3 Layer 6 2.4883 0.6737
NEFM Layer 3 2.3125 0.6736
GAP43 Layer 3 2.1484 0.6735
ELAVL4 Layer 4 2.5176 0.6733
ATP5MD Layer 6 2.0078 0.6731
SYN2 Layer 4 2.1289 0.6719
STMN2 Layer 5 2.4336 0.6719
ATP6V1B2 Layer 5 2.1797 0.6704
ARHGDIG Layer 6 2.4512 0.6703
GABBR2 Layer 4 2.3281 0.6702
MEF2C Layer 6 2.2461 0.6688
ARHGEF9 Layer 4 2.2324 0.6685
GRIN1 Layer 4 2.0859 0.6678
PJA2 Layer 5 2.1582 0.6673
PRKAR1B Layer 4 2.1094 0.6669
GABRB2 Layer 4 2.1191 0.6668
SULT4A1 Layer 6 2.5283 0.6667

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1805
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1805_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1805/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1805/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1805/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1805/report/PD/BN1805_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1805/report/PD/BN1805_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 07:21:46
  • Number of Processes: 10
  • Spending Time: 0h 3m